How to Install Flatpak on Debian

This guide shows how to install Flatpak on Debian so you can run sandboxed desktop apps without changing core system libraries. Common use cases include installing proprietary apps such as Install Discord on Debian and Install Steam on Debian, using Spotify, getting newer releases of tools like GIMP and Blender, and keeping app dependencies isolated from your base system.

By the end, you will have Flatpak installed, Flathub enabled system-wide, and a clear workflow for installing apps in GNOME Software or KDE Plasma Discover, managing apps from the terminal, troubleshooting common issues, and removing Flatpak cleanly if you no longer need it.

Update Debian Before Flatpak Installation

Before installing new packages, refresh the package index and apply available upgrades so Flatpak installs cleanly:

sudo apt update && sudo apt upgrade

Install Flatpak on Debian

Debian includes Flatpak in its standard repositories, but minimal or server installs often omit it. Install it with:

sudo apt install flatpak

Next, verify the installation by checking the version:

flatpak --version

Flatpak 1.16.1

Debian 13 ships Flatpak 1.16.1, Debian 12 ships 1.14.x, and Debian 11 ships 1.10.x. Your output will match your release.

Add the Flathub Repository

Flathub is the primary repository for Flatpak applications, hosting thousands of applications from individual developers, open-source projects, and commercial vendors. To access these applications, add Flathub to your system:

sudo flatpak remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo

This uses the system-wide remote so all users can access Flathub. The --if-not-exists flag avoids errors if the remote is already configured.

Then, verify that Flatpak recognizes Flathub:

sudo flatpak remotes

flathub	system

You should see system next to flathub, confirming the system-wide remote is active.

Apply Flatpak Environment Paths

Flatpak adds desktop entries under standard XDG (X Desktop Group) paths, but your session may cache menus. Log out and back in to reload the desktop session. If applications still do not appear, reboot once to refresh the menu cache:

sudo reboot

If you are on a server or minimal install without a desktop session, you can skip this step.

Install Flatpak Applications with GNOME Software

For users who prefer a graphical interface, GNOME Software provides an easy way to browse, install, and manage Flatpak applications. This section covers setup for GNOME desktop users. For additional GNOME customization options, see Install GNOME Tweaks on Debian.

Install the GNOME Software Flatpak Plugin

First, install the Flatpak plugin to enable Flathub integration in GNOME Software:

sudo apt install gnome-software-plugin-flatpak

After installation, restart GNOME Software or log out and back in for the plugin to take effect.

Browse and Install Applications in GNOME Software

Once the plugin is active, open GNOME Software from your application menu (labeled “Software”). With the Flatpak plugin installed, you can now browse Flathub applications directly:

1. Use the search bar to find a specific application or browse categories.
2. Click an application to view its description, screenshots, and reviews.
3. Click “Install” to download and install the application.

Once installation completes, applications appear in your system’s application menu. From there, you can launch, update, or remove them through GNOME Software.

Install Flatpak Applications with KDE Plasma Discover

If you use KDE Plasma, Discover can manage Flatpak apps alongside Debian packages. If you still need the desktop environment, see Install KDE Plasma on Debian. Install the Flatpak backend:

sudo apt install plasma-discover-backend-flatpak

After installation, restart Discover or log out and back in. Subsequently, Flathub applications will appear alongside distribution packages when searching for software.

Manage Flatpak Applications from Terminal

The Flatpak command-line interface provides full control over application management. Moreover, these commands work regardless of your desktop environment.

Search for Applications

To search for applications by name or keyword, run:

flatpak search gimp

GIMP User Manual	GIMP User Manual	org.gimp.GIMP.Manual	2.10	2.10	flathub
GNU Image Manipulation Program	Create images and edit photographs	org.gimp.GIMP	3.0.6	stable	flathub
Resynthesizer	Resynthesizer GIMP Plugin	org.gimp.GIMP.Plugin.Resynthesizer	3.0	3	flathub

As shown above, the output displays tab-separated columns: application name, description, application ID, version, branch, and source repository. Search results can include manuals or plugins, so use the application ID in the third column (such as org.gimp.GIMP) for installation commands.

Install Applications

Once you find an application, install it using the application ID from the search results:

sudo flatpak install flathub org.gimp.GIMP

During installation, Flatpak will prompt you to confirm and display any required runtimes that will be downloaded.

By default, using sudo installs applications system-wide, making them available to all users. To install for the current user only, drop sudo and add the --user flag: flatpak install --user flathub org.gimp.GIMP

View Application Details

To check details about an installed application, run:

flatpak info org.gimp.GIMP

GNU Image Manipulation Program - Create images and edit photographs

          ID: org.gimp.GIMP
         Ref: app/org.gimp.GIMP/x86_64/stable
        Arch: x86_64
      Branch: stable
     Version: 3.0.6
     License: GPL-3.0+ AND LGPL-3.0+
      Origin: flathub
Installation: system
     Runtime: org.gnome.Platform/x86_64/49
         ...

As you can see, the output shows the application ID, reference path, architecture, branch, version, license, origin repository, installation scope, and runtime dependency. Additionally, fields like commit hash and installation size appear for installed applications.

List Installed Applications

To view all installed Flatpak applications, run:

flatpak list --app

Expected output (example):

GNU Image Manipulation Program	org.gimp.GIMP	3.0.6	stable	system

The --app flag filters the output to show only applications, excluding runtimes and extensions. The final column shows the installation scope (for example, system for system-wide installs). If the list is empty, no Flatpak apps are installed yet.

Update Applications

To update all installed Flatpak applications and runtimes, run:

sudo flatpak update

This updates all system-wide Flatpak apps and runtimes from every configured remote.

Alternatively, to update a specific application only:

sudo flatpak update org.gimp.GIMP

Remove Applications

To uninstall a Flatpak application, run:

sudo flatpak uninstall org.gimp.GIMP

Afterward, clean up unused runtimes and dependencies:

sudo flatpak uninstall --unused

This command removes shared runtimes that are no longer required by any installed application, freeing disk space.

Run Applications from Terminal

To launch a Flatpak application directly from the terminal, run:

flatpak run org.gimp.GIMP

Run this as your normal user (not with sudo). The app window should open, which is useful for debugging or when an application does not appear in your desktop menu.

Flatpak Application Data Location

Flatpak stores per-user data, configuration files, and cache in ~/.var/app/.

System-wide installs keep application files and runtimes under /var/lib/flatpak/, while each app’s user data still lives in ~/.var/app/<app-id>/ (for example, ~/.var/app/org.gimp.GIMP/).

Back up any directories you want to keep before a full removal.

Troubleshoot Common Flatpak Issues

Application Does Not Appear in Menu

If a newly installed application does not appear in your desktop menu, the desktop environment may not have detected the new .desktop file. First, confirm that the app is installed:

flatpak list --app

Expected output (example):

GNU Image Manipulation Program	org.gimp.GIMP	3.0.6	stable	system

When the list is empty, reinstall the app:

sudo flatpak install flathub org.gimp.GIMP

Once the app appears, launch it from the terminal to confirm it works:

flatpak run org.gimp.GIMP

After it launches successfully, log out and back in to refresh the menu. If the menu still does not update, reboot once.

Portal-Related Errors

Flatpak applications use XDG Desktop Portals to interact with system features like file dialogs and screen sharing. If you see errors like the following when launching applications:

No portal found for org.freedesktop.portal.FileChooser
Failed to create portal proxy: No such interface

To fix this, install the portal package for your desktop environment:

sudo apt install xdg-desktop-portal-gtk

However, for KDE Plasma, install the KDE-specific portal instead:

sudo apt install xdg-desktop-portal-kde

After installing the portal package, log out and back in to start the portal services. Then verify the portal is running:

systemctl --user status xdg-desktop-portal

xdg-desktop-portal.service - Portal service
     Loaded: loaded
     Active: active (running)

Permission Issues with Files or Devices

Flatpak applications run in sandboxes with limited filesystem access by default. If an application cannot access specific files or devices, you may see errors like:

Permission denied: /home/user/Documents/file.txt
Cannot access /dev/video0: Operation not permitted

The flatpak override command grants additional access. Grant only what you need, then verify the permission list. For example, to give GIMP access to your home directory:

flatpak override --user --filesystem=home org.gimp.GIMP

Next, verify that Flatpak applied the override:

flatpak info --show-permissions org.gimp.GIMP | grep filesystems

filesystems=xdg-config/GIMP:create;xdg-config/gtk-3.0;/tmp;xdg-run/gvfsd;host;xdg-run/gvfs;home;

The --user flag applies the override for the current user only. To apply system-wide (for all users), replace --user with --system and run with sudo.

Alternatively, for a graphical tool to manage Flatpak permissions, consider installing Flatseal from Flathub.

Remove Flatpak from Debian

If you decide to remove Flatpak from your system, begin by uninstalling all Flatpak applications:

sudo flatpak uninstall --all

This removes every system-wide Flatpak app and runtime. Review the list when prompted before you confirm.

Then, remove the Flathub remote (and any other configured remotes):

sudo flatpak remote-delete flathub

Next, remove Flatpak and the software center plugins:

sudo apt remove --purge flatpak gnome-software-plugin-flatpak plasma-discover-backend-flatpak

Then, clean up orphaned dependencies:

sudo apt autoremove

Remove Flatpak User Data

Flatpak application data remains in ~/.var/app/ after uninstalling applications and Flatpak itself. To remove all Flatpak-related user data:

Warning: This permanently deletes all configuration, saves, and cache data for every Flatpak application. Back up any important data first. This action cannot be undone.

rm -rf ~/.var/app/

Remove System Flatpak Data

System-wide Flatpak apps and runtimes remain in /var/lib/flatpak/ after you remove the package. Remove this directory only if you no longer need any system-wide Flatpak apps or runtimes:

Warning: This permanently deletes all system-wide Flatpak apps and runtimes. If you want a backup, copy the directory first with sudo cp -a /var/lib/flatpak /var/lib/flatpak-backup.

sudo rm -rf /var/lib/flatpak

Verify Flatpak Removal

Finally, confirm Flatpak is no longer installed:

dpkg -l flatpak

dpkg-query: no packages found matching flatpak

If you see a row for flatpak, it is still installed and should be removed before proceeding.

Conclusion

You now have Flatpak installed on Debian with Flathub enabled system-wide, plus the tools to install, update, and troubleshoot apps from either a GUI or the terminal. Use Flatseal for quick permission reviews, and consider Install Firefox on Debian or Install Snapd and Snap Store on Debian if you need alternative packaging options.